The cellular structure of plant tissues is a key parameter for determining their properties. While the morphology of cells can easily be described, few studies focus on the spatial distribution of different types of tissues within an organ. As plants have various shapes and sizes, the integration of several individuals for statistical analysis of tissues distribution is a difficult problem. The aim of this study is to propose a method that quantifies the average spatial organisation of vascular bundles within maize stems, by integrating information from replicated images. In order to compare observations made on stems of different sizes and shapes, a spatial normalisation strategy was used. A model of average stem contour was computed from the digitisation of several stem slab images. Point patterns obtained from individual stem slices were projected onto the average stem to normalise them. Group-wise analysis of the spatial distribution of vascular bundles was applied on normalised data through the construction of average intensity maps. A quantitative description of average bundle organisation was obtained, via a 3D model of bundle distribution within a typical maize internode. The proposed method is generic and could easily be extended to other plant organs or organisms.